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Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Adel A. Rezk1,2,*, Hala A. Amin2
1 Department of Agricultural Biotechnology, College of Agricultural and Food Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
2 Virus and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, 12619, Egypt
* Corresponding Author: Adel A. Rezk. Email: arazk@kfu.edu.sa
(This article belongs to this Special Issue: Plant–Environment Interactions)

Phyton-International Journal of Experimental Botany https://doi.org/10.32604/phyton.2022.024208

Received 26 May 2022; Accepted 19 August 2022; Published online 29 September 2022

Abstract

Citrus Tristeza Virus (CTV), usually occurs in nature as a mixture of genotypes. Six naturally infected citrus (Citrus sinensis) trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt (Sharqia, Qalyubia and Garbia). In this study, RT-PCR, Single-Strand Conformation Polymorphism (SSCP) and nucleotide sequence analysis were used for four independent CTV genomic regions (p65, p18, p20, and p23) to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates. RTPCR products (650 bp) for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing. SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns. Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7% with T36 isolate from USA, Florida. Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate (T36 isolate group), suggesting that they may have originated from closely related ancestors. Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang, p18, p20 and p65, amplified from isolate A3, Sharqia governorate, revealed that the p18, p65, and p20 genes were related to the T3-KB isolate from South Africa with 99%–100% sequence homology. Phylogenetic relationship analysis for p65, p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group. The recombination analysis identified three of six isolates from Sharqia, and Garbia as potential recombinant for p23 gene. The isolates T36 and T3 were identified as major donors for recombination events in isolate A3. Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event. The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.

Keywords

Citrus Tristeza Virus; hotspot region; phylogenetic relationship analysis; sequence comparison; SSCP analysis
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